chr13-50545601-C-T

Variant names:

• chr13-50545601-C-T
• rs279072
• ENST00000469127.6:n.585+39921C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000469127.6(DLEU1):​n.585+39921C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,046 control chromosomes in the GnomAD database, including 35,276 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.68 (35276 hom., cov: 31)
• Consequence: DLEU1 ENST00000469127.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.749
• Publications: 7 publications found

Genes affected

DLEU1 (HGNC:13747): (deleted in lymphocytic leukemia 1)

DLEU7 (HGNC:17567): (deleted in lymphocytic leukemia 7)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000469127.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	ENST00000469127.6	TSL:5	n.585+39921C>T		intron	N/A
	DLEU1	ENST00000470726.7	TSL:5	n.346+112051C>T		intron	N/A
	DLEU1	ENST00000479420.5	TSL:5	n.458-43874C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103182 AN: 151928 Hom.: 35255 Cov.: 31

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.669

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.679 AC: 103248 AN: 152046 Hom.: 35276 Cov.: 31 AF XY: 0.681 AC XY: 50598 AN XY: 74342

African (AFR) AF: 0.621 AC: 25737 AN: 41448

American (AMR) AF: 0.736 AC: 11242 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2459 AN: 3472

East Asian (EAS) AF: 0.862 AC: 4459 AN: 5172

South Asian (SAS) AF: 0.599 AC: 2891 AN: 4826

European-Finnish (FIN) AF: 0.755 AC: 7986 AN: 10582

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46206 AN: 67964

Other (OTH) AF: 0.673 AC: 1417 AN: 2106

Alfa AF: 0.679 Hom.: 58637

Bravo AF: 0.679

Asia WGS AF: 0.726 AC: 2525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.79
PhyloP100		-0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs279072; hg19: chr13-51119737;